Sutton is himself under the spotlight after quitting his role in the run-up to this year's Rio Olympics amid allegations of discrimination and sexism and is the subject of review by British Cycling.
"Our record at British Cycling speaks for itself, our record at (Team) Sky is brilliant, they've endorsed clean cycling from day one," Sutton told BBC Radio Five.
"Knowing Sir Dave Brailsford and the way he works, his work ethic, he's been the big pioneer for clean cycling and we built our success off evidence-based programmes. The evidence will come out and I'm sure that they'll be exonerated."
Sutton said he would he happy to return to work for British Cycling if he is cleared by a separate internal inquiry into his conduct.
"I resigned when I did to take the heat off the team 100 days out from the Olympic Games," he told The Sunday Telegraph. "But I totally refute the claims.
"As I've said all along, I am confident that I will be cleared of any wrongdoing. And if I am, I'd like to think they would ask me to reconsider my resignation."